Mercurial > repos > galaxyp > openms_masscalculator

comparison MassCalculator.xml @ 9:ff18cb79cdd2 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 12:46:33 +0000
parents b3d5b4861942
children 65c6e741ddf3
comparison
equal deleted inserted replaced
8:885e03ff22f1 9:ff18cb79cdd2
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [Utilities]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="MassCalculator" name="MassCalculator" version="2.3.0"> 4 <tool id="MassCalculator" name="MassCalculator" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Calculates masses and mass-to-charge ratios of peptide sequences</description> 5 <description>Calculates masses and mass-to-charge ratios of peptide sequences</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">MassCalculator</token> 7 <token name="@EXECUTABLE@">MassCalculator</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
9 </macros> 11 </macros>
10 <expand macro="references"/> 12 <expand macro="requirements"/>
11 <expand macro="stdio"/> 13 <expand macro="stdio"/>
12 <expand macro="requirements"/> 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
13 <command detect_errors="aggressive"><![CDATA[MassCalculator 15 @EXT_FOO@
16 #import re
14 17
15 #if $param_in: 18 ## Preprocessing
16 -in $param_in 19 #if $in:
20 mkdir in &&
21 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
22 #end if
23 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
24 mkdir out &&
17 #end if 25 #end if
18 26
19 #if $rep_param_in_seq: 27 ## Main program call
20 -in_seq 28
21 #for token in $rep_param_in_seq: 29 set -o pipefail &&
22 #if " " in str(token): 30 @EXECUTABLE@ -write_ctd ./ &&
23 "$token.param_in_seq" 31 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
24 #else 32 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
25 $token.param_in_seq 33 #if $in:
26 #end if 34 -in
27 #end for 35 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
28 #end if 36 #end if
29 #if $param_out: 37 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
30 -out $param_out 38 -out
39 'out/output.${gxy2omsext("txt")}'
40 #end if
41 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
42 | tee '$stdout'
31 #end if 43 #end if
32 44
33 #if $rep_param_charge: 45 ## Postprocessing
34 -charge 46 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
35 #for token in $rep_param_charge: 47 && mv 'out/output.${gxy2omsext("txt")}' '$out'
36 #if " " in str(token):
37 "$token.param_charge"
38 #else
39 $token.param_charge
40 #end if
41 #end for
42 #end if 48 #end if
43 #if $param_format: 49 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
44 -format 50 && mv '@EXECUTABLE@.ctd' '$ctd_out'
45 #if " " in str($param_format): 51 #end if]]></command>
46 "$param_format" 52 <configfiles>
47 #else 53 <inputs name="args_json" data_style="paths"/>
48 $param_format 54 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
49 #end if 55 </configfiles>
50 #end if
51 #if $param_average_mass:
52 -average_mass
53 #end if
54 #if $param_fragment_type:
55 -fragment_type
56 #if " " in str($param_fragment_type):
57 "$param_fragment_type"
58 #else
59 $param_fragment_type
60 #end if
61 #end if
62 #if $param_separator:
63 -separator "$param_separator"
64 #end if
65 #if $adv_opts.adv_opts_selector=='advanced':
66 #if $adv_opts.param_force:
67 -force
68 #end if
69 #end if
70 ]]></command>
71 <inputs> 56 <inputs>
72 <param name="param_in" type="data" format="txt" optional="True" label="Input file with peptide sequences and optionally charge numbers (mutually exclusive to 'in_seq')" help="(-in) "/> 57 <param name="in" argument="-in" type="data" format="txt" optional="true" label="Input file with peptide sequences and optionally charge numbers (mutually exclusive to 'in_seq')" help=" select txt data sets(s)"/>
73 <repeat name="rep_param_in_seq" min="0" title="param_in_seq"> 58 <param name="in_seq" argument="-in_seq" type="text" optional="true" value="" label="List of peptide sequences (mutually exclusive to 'in')" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
74 <param name="param_in_seq" type="text" size="30" label="List of peptide sequences (mutually exclusive to 'in')" help="(-in_seq) "> 59 <expand macro="list_string_val"/>
75 <sanitizer> 60 <expand macro="list_string_san"/>
76 <valid initial="string.printable"> 61 </param>
77 <remove value="'"/> 62 <param name="charge" argument="-charge" type="text" optional="true" value="0" label="List of charge states; required if 'in_seq' is given" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
78 <remove value="&quot;"/> 63 <expand macro="list_integer_valsan"/>
79 </valid> 64 </param>
80 </sanitizer> 65 <param name="format" argument="-format" display="radio" type="select" optional="false" label="Output format ('list': human-readable list, 'table': CSV-like table, 'mass_only': mass values only, 'mz_only': m/z values only)" help="">
81 </param>
82 </repeat>
83 <repeat name="rep_param_charge" min="0" max="1" title="param_charge">
84 <param name="param_charge" type="text" size="30" value="0" label="List of charge states; required if 'in_seq' is given" help="(-charge) ">
85 <sanitizer>
86 <valid initial="string.printable">
87 <remove value="'"/>
88 <remove value="&quot;"/>
89 </valid>
90 </sanitizer>
91 </param>
92 </repeat>
93 <param name="param_format" display="radio" type="select" optional="False" value="list" label="Output format ('list': human-readable list, 'table': CSV-like table, 'mass_only': mass values only, 'mz_only': m/z values only)" help="(-format) ">
94 <option value="list" selected="true">list</option> 66 <option value="list" selected="true">list</option>
95 <option value="table">table</option> 67 <option value="table">table</option>
96 <option value="mass_only">mass_only</option> 68 <option value="mass_only">mass_only</option>
97 <option value="mz_only">mz_only</option> 69 <option value="mz_only">mz_only</option>
70 <expand macro="list_string_san"/>
98 </param> 71 </param>
99 <param name="param_average_mass" display="radio" type="boolean" truevalue="-average_mass" falsevalue="" checked="false" optional="True" label="Compute average (instead of monoisotopic) peptide masses" help="(-average_mass) "/> 72 <param name="average_mass" argument="-average_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compute average (instead of monoisotopic) peptide masses" help=""/>
100 <param name="param_fragment_type" type="select" optional="False" value="full" label="For what type of sequence/fragment the mass should be computed" help="(-fragment_type) "> 73 <param name="fragment_type" argument="-fragment_type" type="select" optional="false" label="For what type of sequence/fragment the mass should be computed" help="">
101 <option value="full" selected="true">full</option> 74 <option value="full" selected="true">full</option>
102 <option value="internal">internal</option> 75 <option value="internal">internal</option>
103 <option value="N-terminal">N-terminal</option> 76 <option value="N-terminal">N-terminal</option>
104 <option value="C-terminal">C-terminal</option> 77 <option value="C-terminal">C-terminal</option>
105 <option value="a-ion">a-ion</option> 78 <option value="a-ion">a-ion</option>
106 <option value="b-ion">b-ion</option> 79 <option value="b-ion">b-ion</option>
107 <option value="c-ion">c-ion</option> 80 <option value="c-ion">c-ion</option>
108 <option value="x-ion">x-ion</option> 81 <option value="x-ion">x-ion</option>
109 <option value="y-ion">y-ion</option> 82 <option value="y-ion">y-ion</option>
110 <option value="z-ion">z-ion</option> 83 <option value="z-ion">z-ion</option>
84 <expand macro="list_string_san"/>
111 </param> 85 </param>
112 <param name="param_separator" type="text" size="30" label="Field separator for 'table' output format; by default, the 'tab' character is used" help="(-separator) "> 86 <param name="separator" argument="-separator" type="text" optional="true" value="" label="Field separator for 'table' output format; by default, the 'tab' character is used" help="">
113 <sanitizer> 87 <expand macro="list_string_san"/>
114 <valid initial="string.printable">
115 <remove value="'"/>
116 <remove value="&quot;"/>
117 </valid>
118 </sanitizer>
119 </param> 88 </param>
120 <expand macro="advanced_options"> 89 <expand macro="adv_opts_macro">
121 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 90 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
91 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
92 <expand macro="list_string_san"/>
93 </param>
122 </expand> 94 </expand>
95 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="false">
96 <option value="out_FLAG">out (Enables the test mode (needed for internal use only))</option>
97 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
98 </param>
123 </inputs> 99 </inputs>
124 <outputs> 100 <outputs>
125 <data name="param_out" format="txt"/> 101 <data name="out" label="${tool.name} on ${on_string}: out" format="txt">
102 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
103 </data>
104 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
105 <filter>OPTIONAL_OUTPUTS is None</filter>
106 </data>
107 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
108 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
109 </data>
126 </outputs> 110 </outputs>
127 <help>Calculates masses and mass-to-charge ratios of peptide sequences 111 <tests>
112 <expand macro="autotest_MassCalculator"/>
113 <expand macro="manutest_MassCalculator"/>
114 </tests>
115 <help><![CDATA[Calculates masses and mass-to-charge ratios of peptide sequences
128 116
129 117
130 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_MassCalculator.html</help> 118 For more information, visit http://www.openms.de/documentation/UTILS_MassCalculator.html]]></help>
119 <expand macro="references"/>
131 </tool> 120 </tool>